LAMMPS (8 Jul 2015)
units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3

comm_modify vel yes
read_data data.swm4-ndp
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2500 atoms
  scanning bonds ...
  1 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  2000 bonds
  reading angles ...
  500 angles
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  3 = max # of 1-4 neighbors
  4 = max # of special neighbors

pair_coeff    1    1      0.210939     3.183950  # ODw ODw
pair_coeff    *   2*      0.000000     0.0

group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES

variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0

neighbor 2.0 bin

timestep 1.0

fix DRUDE all drude C N N D

velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345

delete_bonds ATOMS multi
PPPM initialization ...
  G vector (1/distance) = 0.217457
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.197288
  estimated relative force accuracy = 0.000594128
  using double precision FFTs
  3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 14
  2000 total bonds, 500 turned on, 1500 turned off
  500 total angles, 0 turned on, 500 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off

fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
500 rigid bodies with 2000 atoms
  0.832099 = max distance from body owner to body atom
fix NVE DRUDES nve

compute TEMP all temp/drude

thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20

run 2000
PPPM initialization ...
  G vector (1/distance) = 0.217457
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.197288
  estimated relative force accuracy = 0.000594128
  using double precision FFTs
  3d grid and FFT values/proc = 3375 1000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 24.8361 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] 
       0            0    4568.0415    903.41148      3664.63    623.46454            0    2890.2449    157955.66   -157804.74    244591.08        13824    202.18534    295.64644    14.858785 
      20     1.529202     2882.459    4527.8074   -1645.3484    561.72857            0    600.34616    155114.77   -157922.19    27167.702    14058.741    1013.3326    1438.6699    160.63128 
      40     3.073256    1331.3826    3348.9313   -2017.5487    681.52309            0    553.09465    154668.62   -157920.79     17925.93    14484.215     749.4977    1105.2032    36.587791 
      60     4.584862    297.35979    2604.4137   -2307.0539    583.99971            0     409.0399    154634.74   -157934.83    13017.752    15026.564    582.87312    864.55899    18.335649 
      80     6.053256   -374.31023    2263.3247    -2637.635    534.80338            0    212.27981    154543.18    -157927.9    6155.9261    15645.855    506.53672    755.45209    7.6929084 
     100    7.4787509   -905.58889    1911.7191    -2817.308    532.30405            0    87.570168    154497.48   -157934.66    2149.3099    16288.797    427.84666    639.27768    4.1289101 
     120    8.8570309   -1233.6894    1675.0881   -2908.7775     544.7643            0    59.500519    154422.72   -157935.76     233.4994    16915.818    374.88816    560.54169    2.8313123 
     140    10.102229   -1463.4927    1468.7443    -2932.237    539.69692            0    41.083584    154424.91   -157937.93   -1492.9865    17509.345    328.70799    491.66353    2.1394958 
     160    11.319324   -1695.7535    1385.9603   -3081.7137    552.91518            0    30.022893    154274.72   -157939.37   -3010.4983    18061.925    310.18075      463.968    1.9858941 
     180     12.62008   -1818.1958     1253.169   -3071.3648    559.57456            0     20.01719    154289.67   -157940.63   -3354.4536    18564.877     280.4618    419.57594    1.6725953 
     200    13.836408   -1949.6497    1210.0669   -3159.7167      570.055            0    16.319449    154195.04   -157941.13   -4118.0013    19014.456    270.81546    405.06925     1.766255 
     220    15.032024   -2031.6125    1148.1454   -3179.7579    598.02981            0    30.833041    154127.13   -157935.75   -4514.7299    19406.767     256.9573    384.33701    1.6839691 
     240    16.302775   -2118.6259    1120.0048   -3238.6307     613.2903            0    59.888138     154030.6   -157942.41   -4415.1944     19738.97    250.65937    374.93983    1.5971234 
     260    17.465169   -2203.4348    1065.8476   -3269.2823    614.19171            0    77.619746    153980.69   -157941.79   -4564.2677    20011.077    238.53887    356.80737    1.5247856 
     280    18.614435   -2317.9282    1033.2676   -3351.1958    650.51218            0    126.14976    153811.64   -157939.49   -4722.7543    20224.149    231.24742     345.8479    1.5839508 
     300    19.757547   -2377.6306     992.4842   -3370.1148    688.02217            0    179.77994    153701.18    -157939.1   -4126.4983    20378.439       222.12    332.08757    1.7406267 
     320    20.888309   -2419.6547    1023.0345   -3442.6892    720.31567            0    227.70007    153549.33   -157940.04   -4083.8776    20479.241    228.95722    342.33844    1.7368676 
     340    22.018005   -2456.7661      1048.83   -3505.5961    754.13021            0    264.44865    153415.74   -157939.91   -3894.7125    20529.721    234.73031    351.04714    1.6271854 
     360    23.241519   -2504.7475    1041.9912   -3546.7386    785.42547            0    335.38743    153271.47   -157939.03   -3464.4465    20531.323    233.19976    348.66924    1.7943874 
     380    24.370763   -2596.2223     1000.109   -3596.3313    825.31479            0    390.18238    153129.56   -157941.39   -3355.5804    20490.646    223.82645    334.61119    1.8093168 
     400    25.499192   -2666.6702     1006.474   -3673.1442     865.9858            0    422.51674    152978.57   -157940.21   -3329.4637    20411.001    225.25095    336.79016    1.7220267 
     420    26.635042   -2675.8885    1036.9567   -3712.8452    909.14044            0    490.71452    152826.18   -157938.88   -2907.7096    20294.317    232.07303    346.92895    1.8970394 
     440    27.774963   -2731.5399    1054.4488   -3785.9886    935.99349            0     530.9675    152684.75    -157937.7    -2566.587    20147.094     235.9878    352.84462    1.8021906 
     460    28.922784   -2808.5929    996.20283   -3804.7957     986.6991            0    582.25374    152565.95    -157939.7   -2489.2912    19973.682    222.95224    333.32237    1.7660757 
     480     30.07189     -2862.64    1012.7035   -3875.3436    1005.1596            0    610.07691    152450.62    -157941.2   -2031.6453    19777.635    226.64513    338.80268    1.8767218 
     500    31.210731   -2935.4679    989.23412    -3924.702    1019.9115            0    633.87354     152362.4   -157940.89   -2214.2821    19561.863    221.39263    330.98935    1.7563884 
     520    32.363073   -2989.4684    968.83888   -3958.3072    1057.5825            0    655.88302    152269.68   -157941.45    -2298.887    19328.548    216.82813    324.17678    1.6971802 
     540    33.631173   -3036.6833    1016.2589   -4052.9421    1091.2498            0    658.37327     152140.1   -157942.67    -2240.561    19080.875    227.44082    340.06628    1.7350202 
     560    34.815099   -3093.7794     947.7515   -4041.5309    1141.2318            0     764.1603    151995.79   -157942.71   -1157.5191    18819.961    212.10873    317.02152     1.858938 
     580    36.012327   -3166.4133     987.9563   -4154.3696    1199.2171            0    796.34125    151794.12   -157944.05   -1304.4967    18555.635    221.10665    330.55449    1.7687509 
     600    37.228579   -3194.8572    979.66264   -4174.5199    1206.8265            0    842.68836    151717.96   -157941.99   -843.16439    18290.222    219.25051    327.76152    1.7899831 
     620    38.457464   -3255.2052    965.87596   -4221.0812    1218.8406            0    849.13897    151653.64    -157942.7    -628.0114    18027.862    216.16502    323.08905    1.8846337 
     640    39.700987   -3269.6729    1003.1309   -4272.8038    1273.0417            0    928.68865    151468.54   -157943.07    117.71698    17770.578    224.50275    335.54575    1.9677468 
     660    40.961165   -3293.6967    1002.4504   -4296.1471    1299.7531            0    955.60765    151392.37   -157943.87    207.76414    17523.763    224.35045     335.3089    1.9848634 
     680    42.237597    -3310.539    1011.7934   -4322.3324    1358.9202            0    986.69345    151275.62   -157943.56    677.05046    17289.864    226.44145    338.46824    1.9349743 
     700    43.530486   -3380.6882     976.5597   -4357.2479    1378.7945            0    1003.8845    151205.15   -157945.07    605.30766    17069.732    218.55607    326.63938    1.9523301 
     720    44.837568   -3385.7377    1005.1302   -4390.8679    1389.9512            0    1012.3035    151151.06   -157944.19    817.35931    16863.381    224.95021    336.31657    1.7675955 
     740    46.162222   -3378.6942    1023.8252   -4402.5194    1400.0688            0    1063.4211    151077.64   -157943.65    1513.5741    16671.518    229.13418    342.45655    2.0311926 
     760    47.500172   -3425.4378    1036.4011   -4461.8389    1408.8321            0    1068.7339    151003.75   -157943.15    1350.0894    16496.502     231.9487     346.7108    1.9605952 
     780    48.851472   -3453.9533    1021.8895   -4475.8428    1425.2091            0    1104.5857    150938.44   -157944.08    1801.2205    16339.019    228.70097    341.83264    1.9802343 
     800      50.2129   -3497.6136    979.31494   -4476.9285    1441.1399            0    1119.8292    150908.27   -157946.17    1649.8638    16200.982    219.17269    327.47284    2.1340593 
     820    51.586885   -3545.7792    969.50276    -4515.282    1479.3831            0    1103.1191    150847.98   -157945.76    1410.2174    16081.771    216.97671    324.23659    2.0229826 
     840    52.968935   -3562.4777    972.83071   -4535.3084    1470.5582            0    1079.9217    150857.46   -157943.25    1608.0813    15977.891    217.72151    325.33963    2.0498221 
     860      54.3603   -3569.1307     987.8631   -4556.9938    1446.8392            0    1055.8137    150885.62   -157945.27    1110.2002    15887.947    221.08579     330.4231    1.9689916 
     880    55.752677   -3612.6783    957.13055   -4569.8088    1435.3619            0     1056.264    150883.35   -157944.78    914.27883    15809.361    214.20778    320.06673    2.0614732 
     900    57.105164    -3660.821    939.51428   -4600.3353    1463.6114            0     1070.121    150812.25   -157946.31    1261.3306    15740.285    210.26522    314.20385     1.967446 
     920    58.464501   -3685.0371    941.21956   -4626.2567    1483.8487            0    1096.8187    150737.38   -157944.31    1236.4144    15680.989    210.64687    314.81024      1.89883 
     940     59.82202   -3719.0907    915.61639   -4634.7071    1515.6474            0    1104.1119    150691.39   -157945.86    1066.5855    15632.292    204.91683    306.20627    1.9280979 
     960    61.189826   -3752.7758    893.54303   -4646.3189    1517.1996            0    1125.6182    150656.81   -157945.94    1449.4275    15593.029    199.97676    298.74917    2.0320058 
     980    62.459059   -3752.1139    925.61635   -4677.7302    1528.3468            0    1137.3575    150600.83   -157944.27    1493.1803    15564.263    207.15484     309.5242    2.0018169 
    1000      63.8395   -3737.7642    905.82477    -4643.589     1505.254            0    1110.1192    150686.75   -157945.72    1296.1084    15546.258    202.72544    302.92529    1.9202879 
    1020    65.169118   -3767.2178    892.14155   -4659.3593    1493.2162            0    1085.8721    150707.12   -157945.57    922.80521    15537.177    199.66311    298.24598    2.0980372 
    1040    66.474103   -3783.5702    891.57404   -4675.1442    1484.1631            0    1076.2171    150710.25   -157945.77    707.15481    15535.102     199.5361    298.15469    1.8998396 
    1060     67.68596   -3816.1219    868.55884   -4684.6807    1478.7568            0    1060.3026     150723.2   -157946.94    638.16846    15538.641    194.38525    290.46937    1.8282435 
    1080    69.003517   -3807.3485    875.34276   -4682.6913    1482.2148            0    1055.6143    150725.66   -157946.19    416.14661    15546.427    195.90351    292.75831     1.802085 
    1100    70.315532   -3814.5517    894.42504   -4708.9768    1492.6318            0    1053.4891    150692.22   -157947.31    341.55654    15557.253    200.17416    299.12904    1.8640462 
    1120     71.62724     -3837.42    886.31149   -4723.7315    1497.9422            0    1047.1133    150677.33   -157946.12    4.9308474    15569.465    198.35833    296.42678    1.8247148 
    1140    72.956868   -3802.3965    899.40687   -4701.8034    1479.6329            0    1020.1254    150744.44      -157946   -142.99064    15582.446     201.2891    300.81318    1.8383791 
    1160    74.274932   -3810.7658    902.84695   -4713.6127    1472.5916            0    1018.8174     150740.5   -157945.52    12.783208    15594.928      202.059    301.90406    1.9647721 
    1180    75.595463   -3786.4338    929.44447   -4715.8783    1477.4053            0    1016.2942    150735.81   -157945.39    -53.70556    15606.416    208.01158    310.85718    1.9043666 
    1200    76.915409   -3800.0338    897.43664   -4697.4705    1483.1401            0      1059.31    150706.14   -157946.06    534.37576    15617.028    200.84816    300.11638    1.9100302 
    1220    78.119883   -3799.6824    882.65153   -4682.3339    1488.5302            0    1036.1696    150739.15   -157946.19    155.57627    15628.242    197.53922    295.16257    1.8974641 
    1240    79.419663   -3800.7533    911.18613   -4711.9394    1475.5968            0    1005.3229    150752.61   -157945.47   -457.64009    15638.953    203.92533    304.69739    1.9733514 
    1260    80.721954   -3763.5149    950.12041   -4713.6353    1441.6787            0    964.69517     150825.9   -157945.91   -604.24646    15647.017     212.6389    317.74138    2.0086447 
    1280    82.018768    -3770.742    937.09634   -4707.8384    1445.4659            0    949.37244    150842.61   -157945.28   -993.94783    15650.702    209.72409    313.39122    1.9703726 
    1300    83.314893   -3777.4899    904.34062   -4681.8306    1435.5873            0    967.49755    150860.85   -157945.76   -640.04936    15648.293    202.39329    302.46077    1.8535337 
    1320    84.617907   -3766.6204    885.81908   -4652.4395    1416.0678            0    971.89494    150906.86   -157947.27   -366.46049    15641.654    198.24813    296.26647    1.8149522 
    1340    85.931152   -3774.8032    919.58694   -4694.3901    1425.1776            0    939.16654    150887.07   -157945.81   -950.33698    15631.589    205.80544     307.5014    2.0019282 
    1360    87.242691   -3787.4243    922.65238   -4710.0767    1430.1028            0    964.01827    150842.71   -157946.91   -767.13405    15614.998     206.4915    308.53756    1.9863831 
    1380    88.556261    -3792.754    900.77391   -4693.5279    1420.8035            0    953.09514    150878.52   -157945.95   -1072.9667    15593.378    201.59505    301.19366    1.9946415 
    1400    89.868914   -3772.1032    910.85489   -4682.9581    1401.9732            0    959.20659    150901.09   -157945.23   -640.48972    15566.828    203.85119    304.58411    1.9776581 
    1420    91.085535   -3782.5246    898.64718   -4681.1718    1436.1885            0    1010.9254    150817.16   -157945.45    -21.80524    15536.721    201.11908     300.5555    1.8440133 
    1440    92.406331   -3775.4206    919.73488   -4695.1554    1446.1057            0    1018.1835    150785.23   -157944.68    46.810177    15507.157    205.83855     307.4904     2.123189 
    1460    93.732761   -3757.7457    938.91361   -4696.6593    1451.5945            0    1008.6517    150787.38   -157944.28   -175.88589    15478.297    210.13079    313.97065     2.030827 
    1480    95.057074   -3776.8625     933.4271   -4710.2896    1469.7064            0    1033.8521    150731.34   -157945.19    171.44717    15450.004     208.9029    312.19981    1.8912834 
    1500    96.391192   -3764.5196    945.12068   -4709.6403    1483.0898            0    1052.3029    150699.59   -157944.62    431.18844    15423.716    211.51995    316.14058      1.85565 
    1520    97.721669    -3760.514    960.29952   -4720.8136    1507.6965            0    1068.2902    150648.96   -157945.76    714.27148    15402.108      214.917    321.14587    2.0294443 
    1540    99.056402   -3787.9932    950.73472    -4738.728    1514.4781            0    1058.2368    150635.29   -157946.73    547.92963    15384.955    212.77638    318.01984    1.8639142 
    1560    100.30064   -3822.5612    921.12091   -4743.6821    1519.8628            0    1084.8337     150596.5   -157944.88     479.4088    15370.571    206.14875    308.02344     1.987069 
    1580    101.63827   -3832.4207    936.50822   -4768.9289    1562.5808            0    1124.0034    150490.87   -157946.38    833.06708    15360.019    209.59246    313.15266    2.0528778 
    1600    102.98354   -3862.3688    922.42346   -4784.7923    1571.2038            0    1110.9988     150479.2   -157946.19    674.29885    15354.399    206.44026    308.48417    1.9395764 
    1620    104.32562   -3863.8731    946.37539   -4810.2485    1562.9498            0     1094.323    150478.98    -157946.5   -224.35579    15352.811    211.80075    316.51174    1.9551706 
    1640    105.66368   -3834.5163    952.04367   -4786.5599    1536.5144            0    1078.6783    150544.66   -157946.41   -30.565669    15352.152    213.06933    318.41145    1.9589345 
    1660    107.00124    -3859.131    892.31028   -4751.4413    1515.0462            0    1076.4059    150603.91   -157946.81    227.01045    15352.058    199.70087    298.41871    1.8658052 
    1680     108.2363   -3858.2995     918.6578   -4776.9573    1533.9319            0    1064.9106    150570.69   -157946.49    335.15388    15352.595     205.5975    307.20976    1.9617869 
    1700     109.5659   -3850.0817    929.25672   -4779.3384    1552.5519            0    1094.2161    150519.21   -157945.31    393.76719    15353.331    207.96956    310.72982    2.0330981 
    1720    110.90017    -3890.603    917.87519   -4808.4781    1566.3302            0    1075.6092    150495.91   -157946.33   -76.371955    15355.997    205.42235    306.92393    2.0083539 
    1740    112.13829   -3891.5259    936.37478   -4827.9007    1568.2195            0    1085.8514    150464.14   -157946.11    0.9297943     15358.36     209.5626    313.09836    2.0719603 
    1760    113.46951   -3881.0244    903.38798   -4784.4124    1524.2547            0    1079.0557    150557.47   -157945.19    192.41461    15360.098    202.18008    302.05776    2.0203699 
    1780    114.81068   -3885.7248    910.74799   -4796.4728    1532.8732            0    1055.4583    150560.36   -157945.17   -530.84683    15362.305    203.82727    304.58876    1.8966227 
    1800    116.14689   -3907.0506    885.50025   -4792.5508    1533.7624            0    1068.2841    150550.77   -157945.37    240.13827    15362.751    198.17677     296.0834    1.9671724 
    1820    117.48197   -3898.1244    894.18625   -4792.3107     1521.378            0    1059.1428    150574.05   -157946.88    34.574046    15361.495    200.12072    298.96924    2.0234207 
    1840    118.82815   -3874.3766    895.94028   -4770.3169    1523.7865            0    1077.7882    150573.72   -157945.61    324.16201    15359.092    200.51327    299.59285    1.9530985 
    1860    120.06522   -3892.2617    891.17198   -4783.4337    1526.1544            0    1091.1167    150543.11   -157943.82    574.32363    15357.261    199.44612    297.92332    2.0928308 
    1880    121.40834   -3906.8943    911.93286   -4818.8271    1552.4086            0    1113.1993    150462.35   -157946.79    279.12422     15356.96    204.09245    304.90059    2.0679776 
    1900    122.76151   -3922.7591    879.82965   -4802.5888    1550.6607            0    1108.3657    150485.77   -157947.38    356.47291    15359.386    196.90768    294.18644    1.9563556 
    1920    124.11267   -3960.2437    869.21003   -4829.4537    1521.5339            0    1036.9974     150558.9   -157946.89   -839.29936     15362.76    194.53099    290.66184    1.8802157 
    1940    125.45713    -3954.661    876.75754   -4831.4186    1506.7448            0    1007.0383    150601.14   -157946.34   -1316.6937    15361.338    196.22014    293.17781    1.9123591 
    1960    126.70769   -3938.7558    876.41976   -4815.1756    1481.7627            0    996.84388    150652.15   -157945.93   -887.63902    15352.095    196.14454    293.08662    1.8680915 
    1980    128.05176   -3911.4383    894.43818   -4805.8765    1516.4382            0     1037.517    150585.32   -157945.15   -176.75144    15336.185     200.1771    299.12472    1.8815139 
    2000     129.4091   -3920.2641    888.06919   -4808.3333    1495.9942            0     1040.703    150601.72   -157946.75   -243.72475    15316.676    198.75171    296.94612    1.9653682 
Loop time of 129.409 on 1 procs for 2000 steps with 2500 atoms

Pair  time (%) = 109.108 (84.3128)
Bond  time (%) = 0.0499372 (0.0385887)
Kspce time (%) = 3.30969 (2.55754)
Neigh time (%) = 9.70209 (7.49723)
Comm  time (%) = 0.829103 (0.640684)
Outpt time (%) = 0.00999022 (0.00771987)
Other time (%) = 6.39989 (4.94547)

Nlocal:    2500 ave 2500 max 2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    21780 ave 21780 max 21780 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    2.34087e+06 ave 2.34087e+06 max 2.34087e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2340869
Ave neighs/atom = 936.348
Ave special neighs/atom = 4
Neighbor list builds = 100
Dangerous builds = 6

